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Computational Epigenomics


  • Lutsik P, Slawski M, Gasparoni G, Vedeneev N, Hein M, Walter J.
    MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biology 18:55 


  • Moran S, Martínez-Cardús A, Sayols S, Musulén E, Balañá C, Estival-Gonzalez A, Moutinho C, Heyn H, Diaz-Lagares A, de Moura MC, Stella GM, Comoglio PM, Ruiz-Miró M, Matias-Guiu X, Pazo-Cid R, Antón A, Lopez-Lopez R, Soler G, Longo F, Guerra I, Fernandez S, Assenov Y, Plass C, Morales R, Carles J, Bowtell D, Mileshkin L, Sia D, Tothill R, Tabernero J, Llovet J, Esteller M. Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis. The Lancet Oncology, 17(10):1386-1395 (abstract)
  • Bock C, Halbritter F, Carmona FJ, Tierling S, Datlinger P, Assenov Y, Berdasco M, Bergmann AK, Booher K, Busato F, Campan M, Dahl C, Dahmcke CM, Diep D, Fernández AF, Gerhauser C, Haake A, Heilmann K, ... Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nature Biotechnology, 34(7):726-737 (abstract)
  • Souren NYP, Gerdes LA, Kümpfel T, Lutsik P, Klopstock T, Hohlfeld R, Walter J. Mitochondrial DNA Variation and Heteroplasmy in Monozygotic Twins Clinically Discordant for Multiple Sclerosis. Human Mutation, 37(8):765-775 (abstract)
  • Weigel C, Veldwijk MR, Oakes CC, Seibold P, Slynko A, Liesenfeld DB, Rabionet M, Hanke SA, Wenz F, Sperk E, Benner A, Rösli C, Sandhoff R, Assenov Y, Plass C, Herskind C, Chang-Claude J, Schmezer P, Popanda O. Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis. Nature Communications, 7 (abstract)


  • Schramm A, Köster J, Assenov Y, Althoff K, Peifer M, Mahlow E, Odersky A, Beisser D, Ernst C, Henssen AG, Stephan H, Schröder C, Heukamp L, Engesser A, Kahlert Y, Theissen J, Hero B, Roels F, Altmüller J, Nürnberg P, Astrahantseff K, Gloeckner C, De Preter K, Plass C, Lee S, Lode HN, Henrich KO, Gartlgruber M, Speleman F, Schmezer P, Westermann F, Rahmann S, Fischer M, Eggert A, Schulte JH. Mutational dynamics between primary and relapse neuroblastomas. Nature Genetics, 47(8):872-877 (abstract)
  • Liesenfeld DB, Habermann N, Toth R, Owen RW, Frei E, Böhm Ü, Schrotz-King P, Klika KD, Ulrich CM. Changes in urinary metabolic profiles of colorectal cancer patients enrolled in a prospective cohort study (ColoCare). Metabolomics, 11(4):998-1012 (abstract)


  • Kunz J, Bandapalli OR, Rausch T, Stuetz A, Pechanska P, Assenov Y, Eilers J, Orlova E, Sagi J, Stanulla M, Schrappe M, Handgretinger R, Kirschner-Schwabe R, Hof J, Eckert C, Avigad S, Koehler R, Muckenthaler MU, Korbel J, Kulozik AE. Targeted Deep Sequencing of Genetic Alterations Identified By Whole Exome Sequencing Reveals Clonal Evolution in Pediatric T-Lymphoblastic Leukemia. Blood, 124(21):491-491 (abstract)
  • Ecsedi S, Hernandez-Vargas H, Lima SC, Vizkeleti L, Toth R, Lazar V, Koroknai V, Kiss T, Emri G, Herceg Z, Adany R, Balazs M. DNA methylation characteristics of primary melanomas with distinct biological behaviour. PLoS ONE, 9(5):e96612 (abstract)
  • Assenov Y*, Müller F*, Lutsik P*, Walter J, Lengauer T, Bock C. Comprehensive analysis of DNA methylation data with RnBeads. Nature Methods, 11(11):1138-1140 (abstract)
  • Brocks D, Assenov Y, Minner S, Bogatyrova O, Simon R, Koop C, Oakes CC, Zucknick M, Lipka DB, Weischenfeldt J, Feuerbach L, Cowper-Sal R, Lupien M, Brors B, Korbel J, Schlomm T, Tanay A, Sauter G, Gerhäuser C, Plass C. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Reports, 8(3):798-806 (abstract)
  • Oakes CC, Claus R, Gu L, Assenov Y, Hüllein J, Zucknick M, Bieg M, Brocks D, Bogatyrova O, Schmidt CR, Rassenti L, Kipps TJ, Mertens D, Lichter P, Döhner H, Stilgenbauer S, Byrd JC, Zenz T, Plass C. Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia. Cancer Discovery 4(3):348-361 (abstract)


  • Rakosy Z, Ecsedi S I, Toth R, Vizkeleti L, Hernandez-Vargas H, Lazar V, Emri G, Szatmari I, Herceg Z, Adany R, Balazs M. Integrative genomics identifies gene signature associated with melanoma ulceration. PLoS ONE, 8(4)::e54958 (abstract)
  • Sandoval J, Mendez-Gonzalez J, Nadal E, Chen G, Carmona FJ, Sayols S, Moran S, Heyn H, Vizoso M, Gomez A, Sanchez-Cespedes M, Assenov Y, Müller F, Bock C, Taron M, Mora J, Muscarella LA, Liloglou T, Davies M, Pollan M, Pajares MJ, Torre W, Montuenga LM, Brambilla E, Field JK, Roz L, Lo Iacono M, Scagliotti GV, Rosell R, Beer DG, Esteller M. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. Journal of Clinical Oncology, 31(32):4140-4147 (abstract)


  • Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics, 7(12):1355-1367 (abstract)
  • Doncheva NT, Assenov Y, Domingues FS, Albrecht M. Topological analysis and interactive visualization of biological networks and protein structures. Nature Protocols, 7(4):670-685 (abstract)
  • Feuerbach L, Halachev K, Assenov Y, Muller F, Bock C, Lengauer T. Analyzing epigenome data in context of genome evolution and human diseases. Methods in Molecular Biology, 856(4):431-467 (abstract)
  • Calvanese V, Fernandez AF, Urdinguio RG, Suarez-Alvarez B, Mangas C, Perez-Garcia V, Bueno C, Montes R, Ramos-Mejia V, Martinez-Camblor P, Ferrero C, Assenov Y, Bock C, Menendez P, Carrera AC, Lopez-Larrea C, Fraga MF. A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Research, 40(1):116-131 (abstract)
  • Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, Yamamoto H, Hidalgo M, Tan AC, Galm O, Ferrer I, Sanchez-Cespedes M, Villanueva A, Carmona J, Sanchez-Mut JV, Berdasco M, Moreno V, Capella G, Monk D, Ballestar E, Ropero S, Martinez R, Sanchez-Carbayo M, Prosper F, Agirre X, Fraga MF, Grana O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M. A DNA methylation fingerprint of 1628 human samples. Genome Research, 22(2):407-419 (abstract)
  • Vizkeleti L, Ecsedi S, Rakosy Z, Begany A, Emri G, Toth R, Orosz A, Szollosi AG, Mehes G, Adany R, Balazs M. Prognostic relevance of the expressions of CAV1 and TES genes on 7q31 in melanoma. Frontiers in Bioscience, 4:1802-1812 (abstract)


  • Toth R, Fiatal Sz, Petrovski BE, McKee M, Adany R: Combined effect of ADH1B rs1229984, rs2066702 and ADH1C rs1693482/rs698 alleles on alcoholism and chronic liver diseases, Disease Markers, 31(5):267-277 (abstract)
  • Fiatal S, Szigethy E, Szeles G, Toth R, Adany R: Insertion/deletion polymorphism of angiotensin-1 converting enzyme is associated with metabolic syndrome in Hungarian adults. JRAAS, 12(4):531-538 (abstract)


  • Toth R, Pocsai Z, Fiatal S, Szeles G, Kardos L, Petrovski B, McKee M, Adany R. ADH1B*2 allele is protective against alcoholism but not chronic liver disease in the Hungarian population. Addiction, 105:891-896 (abstract)


  • Lazar V, Ecsedi S, Szollosi AG, Toth R, Vizkeleti L, Rakosy Z, Begany A, Adany R, Balazs M. Characterization of candidate gene copy number alterations in the 11q13 region along with BRAF and NRAS mutations in human melanoma. Modern Pathology, 22:1367-1378 (abstract)


  • Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics, 24(2):282-284 (abstract)


  • Ramírez F, Schlicker A, Assenov Y, Lengauer T, Albrecht M. Computational analysis of human protein interaction networks. Proteomics, 7(15):2541-2552 (abstract)
  • Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Ólason Pí, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A. The implications of alternative splicing in the ENCODE protein complement. PNAS, 104(13):5495-5500 (abstract)
  • Salamat-Miller N, Fang J. Seidel CW, Assenov Y, Albrecht M, Middaugh CR. A network-based analysis of polyanion-binding proteins utilizing human protein arrays. Journal of Biological Chemistry, 282(14):10153-10163 (abstract)


  • Salamat-Miller N, Fang J, Seidel CW, Smalter AM, Assenov Y, Albrecht M, Middaugh CR. A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays. Molecular & Cellular Proteomics, 5(12):2263-2278 (abstract)

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